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I.
Introduction

Hammerhead
ribozymes are small, catalytic RNAs that undergo self-cleavage of
their own backbone to produce two RNA products. All hammerhead ribozymes
contain three base-paired stems and a highly conserved core of residues
required for cleavage.The
cleavage reaction proceeds by an attack of a 2' hydroxyl oxygen of
a catalytic site cytosine on the phosphorus atom attached to the 3'
carbon of the same residue. This breaks the sugar phosphate backbone
and produces a 2', 3' cyclic phosphate. As for protein ribonucleases,
a metal ion bound in the active site (Mg++)
stabilizes the ionized form of the 2' hydroxyl oxygen, promoting the
catalytic attack.

The wishbone-shaped
structure at left is is a hammerhead ribozyme in which a portion of
the RNA has been substituted with a stretch
of DNA
that acts as an inhibitor of catalysis, due to the absence of 2' hydroxyl
groups in DNA (Pley, et al., 1994). The structure was the
first described for a hammerhead ribozyme.

II. Structure
of the RNA-DNA Hammerhead Ribozyme

Stem I is formed
by base pairing of complementary nucleotides through Watson-Crick
hydrogen bonding. The 5' phosphate and
3' oxygen atoms mark the beginning and
end of the ribozyme and are juxtaposed at the top of Stem
I.

Stem II lies
opposite Stem I in the other branch of
the "wishbone." It also is formed by standard Watson-Crick
base pairing and is capped by a four base loop
at the top of the branch.

Stem III
is formed by Watson-Crick base pairing and forms the base of the "wishbone."
In a standard ribozyme, formed by a continuous RNA molecule instead
of an RNA-DNA, two-chain hybrid, the nucleotides
at the base of Stem III are connected
by a short loop (see below).

The base sequences
of the three stems can vary, depending on the hammerhead ribozyme
under consideration. The only sequence restriction is that Watson-Crick
base complementarity is maintained so that stem hydrogen bonding can
form. The central core sequence, however, is highly conserved between
ribozymes and is essential for ribozyme catalytic activity. The core
contains two domains.

Domain
1 of the core comprises a CUGA
sequence, the uridine turn, that
follows Stem I.

Domain
2 is formed by non-Watson Crick base
pairing, and connectsStem
II and Stem III.

C17
is the conserved residue at which strand cleavage takes place (see
Introduction).

III. Structure
of an All-RNA Hammerhead Ribozyme

Scott,
et al. (1995) succeeded in determining the structure of a
hammerhead ribozyme that comprises an RNA enzyme
strand complexed with an RNA substrate strand,
shown at left.

The
substrate is not cleaved because the cleavage
site cytosine bears a 2' methoxyl group instead of the reactive
2' hydoxyl (see Introduction).

Despite different crystallization conditions,
loop position, and phosphate backbone connectivity,
the structure of the all-RNA ribozyme is remarkably similar to the
RNA-DNA hybrid discussed above, with the same stems
(I, II,
III), conserved core domains (CUGA
and Domain 2), and catalytic
C17. This suggests that these conformations likely represent
the genuine structure of hammerhead ribozymes in solution.